Arranging atoms in an orderly manner at the atomic scale to create stable polyatomic structures is a very challenging task. In this study, we have developed three-dimensional confinement areas on the two-dimensional surface by creating regional defects. These areas are composed of vertically stacked graphene layers, where Ni and Fe atoms are anchored concentrically to form axial dual atomic sites in high yield. These sites can be used to produce tunable syngas through the electroreduction of CO2. Theoretical calculations indicate that the Ni sites vertically regulate the charge distribution of the adjacent Fe sites in the layer below, resulting in a lower d-band center. This, in turn, weakens the adsorption of the *CO intermediate and inhibits the production of H2 at the Fe site. Our research presents a novel approach for concentrated creation of dual atomic sites by building a confinement-selective surface.